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Kalenić et al.
The role of microbiology laboratory in healthcare-associated infection prevention
International Journal of Infection Control
www.ijic.info
ISSN 1996-9783
extended abstract
The role of the microbiology laboratory
in healthcare-associated infection prevention
Smilja Kalenić, Ana Budimir
Croatian Society for medical Microbiology and Parasitology,
Section for Healthcare-associated Infection Prevention and Control, Zagreb, Croatia
doi: 10.3396/ijic.V5i2.014.09
Introduction
Healthcare associated infections (HAI) are a big
problem worldwide, increasing morbidity and mortality
of hospitalized patients, as well as increasing cost
of healthcare. Many hospitals throughout the world
have good systems for HAI prevention and control,
but others have not and are forced to develop such
systems nowadays. Having microbiology laboratory
as a part of the hospital diagnostic laboratories, is
a huge advantage for HAI prevention and control.
Ideally, a microbiology laboratory should be set up
inside the hospital, working every day on a 24 hour
basis. If it is not possible, then hospital should contract
microbiology services with the geographically nearest
laboratory.
Microbiology laboratory has two main functions in
the hospital: one is diagnosis of infection in individual
patient, directly related to the patient care and the
other is support to the HAI prevention and control.
But the first role – diagnosis of infection – has also a
function in HAI prevention: if the etiological diagnosis
of infection is rapid and accurate, the patient will be
treated properly at the beginning of infection, so time
of dispersing microorganisms will be shorter.
Every microbiology laboratory should have quality
assurance procedures in place, and if possible, external
quality control of main procedures performed by
Int J Infect Control 2009, v5:i2 doi: 10.3396/ijic.V5i2.014.09
the laboratory. Dramatic changes in microbiological
diagnostic techniques in the last decades – rapid
diagnostic methods and precise typing methods –
have emphasised even more the role of microbiology
laboratory.
Diagnosis of infections
For the accurate etiological diagnosis of infection
several conditions should be fulfilled: first, clinician
should put right indication for this diagnostics;
furthermore, the right sample should be taken; then,
all data needed for the laboratory should be put on the
request (name of the patient and the physician, location
of the patient, date and time of specimen collection,
working diagnosis or differential diagnosis, underlying
patient conditions, antimicrobial chemotherapy if
already instituted).
Specimens sent to the microbiology laboratory have
to be taken on the right time (depending on the
pathogenesis of the infection), from appropriate sites
using proper techniques, in a quantity that will ensure
good workout in the laboratory. Transport conditions
from the patient to the laboratory are to be carefully
maintained. Microbiology laboratory staff can assist in
ensuring good specimens by educating clinical staff.
Rapid and accurate diagnosis and sensitivity test are
of outmost importance for the direct patient care. In
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The role of microbiology laboratory in healthcare-associated infection prevention
the laboratory methodology it is necessary to provide
rapid tests (like pneumococcal urine antigen in the
case of community acquired pneumonia, or rotavirus
latex agglutination for detection of rotavirus in faeces
etc). For diagnosis to be accurate, laboratory has to
develop procedures for quality assurance and has
external quality control system in function.
Microbiology laboratory should be able to examine
blood, cerebrospinal fluid, urine, stool, wound
exudate or swab, respiratory secretions, and perform
basic serological tests (HIV, HBV, HCV, influenza).
Microbiological laboratory should be able to identify at
least the following bacteria and fungi: Staphylococcus
aureus, Escherichia coli, Group A streptococci, Group B
streptococci, enterococci, Streptococcus pneumoniae,
Haemophilus influenzae, Neiserria meningitidis
and Neiserria gonorrhoeae, Salmonella, Shigella,
Campylobacter jejuni/coli, Clostridium difficile,
Pseudomonas aeruginosa, Klebsiella pneumoniae,
other enterobacteria, Candida albicans, aspergilli
(and other, depending on local epidemiological
situation); also, it should be able to diagnose specific
viral infections (eg some of viruses causing diarrhoeal
diseases), but mostly using serological methods (HIV,
HBV, HCV, influenza, or other viruses, depending on
local epidemiological situation).
Methods used in the diagnosis of infections are:
1. Classical methods, like
• Direct smear
• Culture
• Antigen detection
• Serological tests
2. Molecular methods (not very often used in
routine work)
• Hybridization
• Amplification
• Real-time amplification
As identification of the infectious agent is gradual,
the laboratory has to communicate with the attendant
clinician preliminary and definite diagnosis, as well as
sensitivity test results (Figure 1).
For sensitivity testing the most used method is discdiffusion, although nowadays many laboratories are
using automated methods. Some laboratories use
MIC determination, either by classical MIC dilution
techniques or by E-tests. Sensitivity test results are
used immediately for the patient care. Adequate
antimicrobial therapy leads to better outcomes and is
vital for individual patient care, as well as the decrease
of microorganism transmission to other patients. But
also, laboratory should perform periodical reports of
Attendant
Physician
Microbiologist
Specimen
Transport
Taking
Specimen
Patient:
Indication
Treatment
Constant
Information
Flow
Primary
Workout
Culture
Identification
Sensitivity
Written
Report
Figure 1. Communication between attendant physician and microbiologist for ethiological diagnosis of infection
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The role of microbiology laboratory in healthcare-associated infection prevention
sensitivity of bacteria (broken down by bacteria and
specimen) isolated in patient on the specific ward
(unit) – and this would mostly be intensive care unit –
for the design of empiric therapy of infections in that
specific ward (unit).
The role in HAI prevention
1. Rapid communication
Infection control practitioner’s (ICP) day should ideally
start in the microbiology laboratory, personally or
virtually. This would be the best and the most rapid
communication of everyday infectious problems ICP
can encounter in the hospital. If this is not possible,
then laboratory workers should communicate
by phone or personally with the ICP every new
important isolated pathogen in patients. This rapid
communication is crucial and is the base of any good
collaboration between microbiology laboratory and
infection control.
2. Accurate speciation and typing of isolated pathogen
To be useful for epidemiological studies of HAI,
isolated bacterial strains should be identified to the
species level. Many times this is enough for definite
epidemiological analysis of small clusters or even
outbreaks of HAI if pathogenic bacteria are involved
(e.g. Salmonella Enteritidis food poisoning outbreak
originated from hospital kitchen). But, if the isolated
bacteria are only opportunistic pathogens (e.g. S.
aureus, E. coli, Enterobacter cloacae, enterococci etc)
it is necessary to type those isolates to be sure that
the cluster or outbreak patients are connected. To
type means to determine characteristics which differ
between different strains of the same bacterial species.
Namely, the individual bacteria inside the same species
could differ in their genome as much as 30%, and in
the individual bacterial clone (clone= offsprings of the
common ancestor) these differences are very small or
even non-existent.
Typing of bacteria is possible by several methods. Main
characteristics of typing methods are:
• Typability, i.e., the method types most or all
strains of the same species
• Discriminatory power, i.e., the method
differentiates between different types
• Inter/intra laboratory reproducibility, i.e., the
method provides the same typing results in
repeated testing on same or different sites
Int J Infect Control 2009, v5:i2 doi: 10.3396/ijic.V5i2.014.09
• The method has to be simple, unambiguous to
interpret, and inexpensive
There are two groups of typing methods:
a) phenotyping
b) genotyping
a) Phenotyping means that we are determining
characteristics that are expressed in the bacterial
culture, like:
• Antigenic structure (serotyping)
• Physiologic properties/metabolic reactions
(biotyping)
• Susceptibility to antimicrobial agents
(resistotyping)
• Susceptibility to colicines (colicinotyping), or
• Susceptibility to bacteriophages (phage typing)
Very important limiting factor of phenotypic methods
is the fact that bacterial genes are not always expressed
and so two phenotypically different strains can
actually have the same genetic background or two
phenotypically identical strains can actually differ
genetically. The other limiting factor is that sometimes
one unique phenotype is widespread and frequent, and
in that cases genotyping will be required for outbreak
management.
b) Genotyping can demonstrate the relatedness
or difference between two isolates of the same
species very precisely. Diagnosis can be rapid
– because it is not dependent on waiting for
bacterial growth in cultures. Genotyping requires
sophisticated and expensive equipment and
materials and also well trained staff. Genotyping
methods are either imaging (based on restriction of
part or whole genome with the endonucleases and
electrophoresis of fragments), or sequence-based
(which means definite biological information and
is more and more used).
Some imaging methods have a low reproducibility,
especially in interlaboratory comparisons, and
interpretation of results is neither always simple nor
unambiguous.
Genotyping methods are not very often used in routine
microbiology laboratory. Therefore it is important for
a hospital laboratory to be connected with research
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laboratories in the country, or other types of central
laboratories that are able to perform such genotyping
in the time of the outbreak.
3. Participation in outbreak management
The early isolation of a new or unusual microorganism
enables the ICP to take appropriate measures to stop
it from spreading at the very beginning. Any new
isolates should be reported immediately to the wards
and the ICP. Laboratory staff may also report clustering
of infections (two related isolates in different patients
in the same time frame), which then enables ICP to go
and check these cases.
In an outbreak suspected to be caused by one and
the same causative agent it is very helpful (sometimes
even necessary) for the agent to be isolated, identified
to the species level and also typed.
Bacterial typing determines if two or more strains are
really related and if they differ from strains that are
not epidemiologically connected. If two (or more)
strains are unrelated, the patients do not belong to the
same outbreak, and it is very simple to interpret that
pattern. But, if two (or more) strains are related after
we performed strain typing it is very difficult to say that
the patients are involved in an outbreak without sound
epidemiological analysis.
Kalenić et al.
Sometimes during the outbreak analysis, epidemiologist
would ask laboratory some additional types of tests,
to clarify the situation. These can be for example
microbiological tests of blood products, environmental
surfaces, disinfectants and antiseptics, air, water, hands
of personnel, nostrils of personnel.
4. Participation in HAI surveillance
Surveillance of HAI is an important task of a well
organized infection control. If outcome surveillance
is performed, inherent to some infection definitions
(BSI, UTI) is an isolation of the causative organism,
but also important in all other infection definitions.
Furthermore, in alert or multi-drug resistant (MDR)
organisms surveillance the role of microbiology
laboratory is crucial. The most important ‘alert’
microorganisms are:
• Methicillin-resistant Staphylococcus aureus (MRSA)
• Vancomycin-intermediate S. aureus (VISA)
• Vancomycin-resistant enterococci (VRE)
• MDR Pseudomonas aeruginosa
• MDR Acinetobacter baumannii
• MDR Mycobacterium tuberculosis
• ESBL enterobacteria
• Clostridium difficile
MRSA infections in surgical intensive care unit
Figure 2. MRSA infections in Surgical Intensive Care Unit, time series
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The microbiology laboratory should produce routine
reports to allow the ICP to make graphs for specific
pathogens, wards, and groups of patients. A ‘baseline
incidence’ can be then established and any new isolate
incidence can be compared with this incidence. If such
graphs are in the form of time series, they will enable
the ICP to discover the beginning of an outbreak earlier
than it would be possible clinically (Figure 2).
Periodic reports also demonstrate trends of specific
pathogens and can be very useful in planning preventive
measures. Microbiology laboratory also participates in
routine process surveillance monitoring sterilization,
monitoring dialysis fluid. Sometimes it may be useful
to routinely monitor some other processes, like infant
formula and instrument disinfection.
5. Participation in resistance surveillance
The surveillance of bacterial resistance to antimicrobial
agents is very important task of microbiological
laboratory. It serves to an antibiotic management team
in hospitals, to make policies for antibiotic use with
the ultimate goal to decrease this resistance. Resistance
reports are usually periodical (yearly reports) and it is
very useful to have resistance surveillance organised
on regional or country or even international level, to
cope with the resistance development on a broader
scale (for example European Antimicrobial Resistance
Surveillance System).
6. Education of HAI prevention personnel and other
healthcare workers
Microbiologist acts also as an educator for infection
control personnel, first about characteristics of
microorganisms that are important for epidemiology of
infections, then about normal flora, difference between
contamination, colonisation and infection with
specific organisms, furthermore about interpretation of
microbiological reports and charts.
Microbiology laboratory staff serves also as educators
to all other healthcare workers, about specimen taking
and transport and also interpretation of microbiology
findings. Microbiology laboratory serves as education
point for basic clinical microbiology for medical and
nursing students.
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Kalenić et al.
7. Microbiologist as a member of Infection Control
Committee (ICC)/Infection Control Team (ICT) and
Antibiotic Committee (AC)
As microbiologist has specialist knowledge necessary
for infection control and antibiotic use he/she is an
indispensable member of ICC/ICT and AC in hospitals.
Other members of ICC and AC in hospital do not have
the knowledge of microbiology. It is not surprising then,
that in US almost half of the ICC chairs are laboratory
personnel.
It is also important that the microbiologist is a
medical doctor, because he/she will thus understand
pathogenesis of infection as well as pathogenesis
of HAI, not only characteristics of an organisms,
will be able to understand pharmacokynetics and
pharmacodynamics of antimicrobial agents - and will
be able to communicate with clinical and nursing
colleagues on the same level of understanding disease,
therapy and epidemiology.
Only exceptionally, if there is no medical doctor
available, a properly educated scientist could be
microbiologist too, but in that situation he/she has
to be very closely connected with infectious disease
specialist.
Conclusion
Microbiology laboratory is becoming an integral part
of HAI prevention programmes. The emergence of
new pathogens, and new resistances in old pathogens,
makes microbiology laboratory indispensable for
successful prevention of HAI, not only outbreaks, but
sporadic cases too.
Different typing methods, available on site or in
the central laboratory of the country, are necessary
for outbreak management. As microbiology and
laboratory methods are developing very fast, there is
a sound need for a specialist microbiologist to be a
part of the infection control team, infection control
committee and antibiotic committee. Only very
close communication, collaboration and cooperation
between microbiology laboratory and infection control
personnel can fulfil the duties of successful infection
prevention and control in healthcare institutions.
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